RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780935|ref|YP_003065348.1| rare lipoprotein A [Candidatus Liberibacter asiaticus str. psy62] (276 letters) >3d30_A YOAJ, expansin like protein; peptidoglycan associated protein, unknown function, MLTA, bacteria autolysis, peptidoglycan-binding protein; 1.90A {Bacillus subtilis} PDB: 2bh0_A Length = 208 Score = 46.9 bits (111), Expect = 5e-06 Identities = 20/100 (20%), Positives = 33/100 (33%), Gaps = 11/100 (11%) Query: 90 GMASWYGKAFHGRLTANGEVYGTEYITAAHPTLPLP---------SYVRVTNMENGISLV 140 G A++ G + G + ITA +P SY+ V Sbjct: 9 GYATYTGSGYSGGAFLLDPIPSDMEITAINPADLNYGGVKAALAGSYLEVEG--PKGKTT 66 Query: 141 VRVNDRGPYHSNRLIDLSNAAAKILRVEERGVSKVHVEYL 180 V V D P + +DLS A + + + G + + Sbjct: 67 VYVTDLYPEGARGALDLSPNAFRKIGNMKDGKINIKWRVV 106 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 39.9 bits (93), Expect = 7e-04 Identities = 52/353 (14%), Positives = 91/353 (25%), Gaps = 166/353 (47%) Query: 23 SSCFFSSTYKDD-KL-----------EYFPE-----SMYG-------VTASDRIVSGKRV 58 +S F + + + +L +YF E Y +++ + R Sbjct: 142 NSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRT 201 Query: 59 PRGGGRYFLGKPYQIMGRWY-----VP-RQYTAYAAV-----G---MASWY------GK- 97 + F + I+ W P + Y + G +A + G Sbjct: 202 TLDAEKVF-TQGLNIL-EWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFT 259 Query: 98 --AFHGRLT-ANGEVYGTEYITAA-----------------------------H---PTL 122 L A G G +TA + P Sbjct: 260 PGELRSYLKGATGHSQGL--VTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNT 317 Query: 123 PLPSYVRVTNMENGIS-----LVVRVNDRG-PYHS-NRLIDLSNAAAKILRVEERGVSKV 175 LP + ++EN L + ++ +N L ++ V Sbjct: 318 SLPPSILEDSLENNEGVPSPMLSI----SNLTQEQVQDYVNKTN---SHLPAGKQ----V 366 Query: 176 HVEYLGMALLNGMDQEYLRSTVMVNSATVLPLGCQYREEIVVI-PYL-LTRSRTVHLNNC 233 + +L+NG +VV P L LN Sbjct: 367 EI-----SLVNGAKN------------------------LVVSGPPQSL-----YGLN-- 390 Query: 234 DDDSLQKQREISLRERKKS-----NLIPLPNGYSPPRKMGKI-----PIPSRF 276 ++LR+ K + IP +S RK+ K P+ S F Sbjct: 391 ----------LTLRKAKAPSGLDQSRIP----FS-ERKL-KFSNRFLPVASPF 427 Score = 33.8 bits (77), Expect = 0.041 Identities = 13/79 (16%), Positives = 27/79 (34%), Gaps = 27/79 (34%) Query: 148 PYHSNRLIDLSNAAAKIL-RVEERGVSKVHVEYLGMALL---NGMDQEYLRS-------- 195 P+HS+ L+ A+ I + + V + + + + + +G D LR Sbjct: 426 PFHSHLLVP---ASDLINKDLVKNNV-SFNAKDIQIPVYDTFDGSD---LRVLSGSISER 478 Query: 196 ------TVMVN--SATVLP 206 + V + T Sbjct: 479 IVDCIIRLPVKWETTTQFK 497 Score = 33.8 bits (77), Expect = 0.048 Identities = 51/304 (16%), Positives = 80/304 (26%), Gaps = 130/304 (42%) Query: 12 GSVVCVVVLGMSSCFFSSTYKDDKLEYFPESMYGVTASDRIVS---------G---KRV- 58 GS+ V+++ +S F +S ++ + PE G A D + G V Sbjct: 14 GSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVE 73 Query: 59 PRGGGRY--------------FLG--------------------KPYQIMGRWYVPRQYT 84 P G++ +L K +++ + Y T Sbjct: 74 PSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELI-KNY----IT 128 Query: 85 AYAAVG--MASWYGKAF-------HGRLTA------NGEVYGTE----YITAAHPTLPLP 125 A A + +L A N + Y E Y T Sbjct: 129 ARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQT-------YH 181 Query: 126 SYVRVTNMENGISLVVRVNDRGPYHSNRLIDLSNAAAKILRVEERGVSKVHVEYLG-MAL 184 V L+ + L +L KV + L + Sbjct: 182 VLVG--------DLIKFS-------AETLSELI--------RTTLDAEKVFTQGLNILEW 218 Query: 185 LNGM----DQEYLRSTVMVNSATV-LPL-G----CQYREEIVVIPYL-LT----RSR--- 226 L D++YL S + PL G Y +V L T RS Sbjct: 219 LENPSNTPDKDYLL------SIPISCPLIGVIQLAHY---VVTAKLLGFTPGELRSYLKG 269 Query: 227 -TVH 229 T H Sbjct: 270 ATGH 273 >2eab_A Alpha-fucosidase; glycoside hydrolase; 1.12A {Bifidobacterium bifidum} PDB: 2eac_A* 2ead_A* 2eae_A* Length = 899 Score = 33.3 bits (75), Expect = 0.068 Identities = 17/122 (13%), Positives = 32/122 (26%), Gaps = 9/122 (7%) Query: 43 MYGVTASDRIV-------SGK--RVPRGGGRYFLGKPYQIMGRWYVPRQYTAYAAVGMAS 93 ++G + +R+ +G G K + +Q A Sbjct: 63 VWGEVSRERVTFNEETLWTGGPGSSTSYNGGNNETKGQNGATLRALNKQLANGAETVNPG 122 Query: 94 WYGKAFHGRLTANGEVYGTEYITAAHPTLPLPSYVRVTNMENGISLVVRVNDRGPYHSNR 153 + N +G Y+ + Y R N+ G + V +D Y Sbjct: 123 NLTGGENAAEQGNYLNWGDIYLDYGFNDTTVTEYRRDLNLSKGKADVTFKHDGVTYTREY 182 Query: 154 LI 155 Sbjct: 183 FA 184 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 29.8 bits (66), Expect = 0.67 Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%) Query: 234 DDDSLQKQREISLRERKKSNLI-P-LPNGYSPPRK 266 DD ++ + E S+ E LI P L NGY+P +K Sbjct: 886 DDKDVKAKYETSILEHSGIRLIEPELFNGYNPEKK 920 >2rdy_A BH0842 protein; PSI-II, structural genomics, protein structure initiative, NEW YORK SGX research center for structural genomics; 2.03A {Bacillus halodurans c-125} Length = 803 Score = 28.6 bits (63), Expect = 1.8 Identities = 10/49 (20%), Positives = 15/49 (30%) Query: 111 GTEYITAAHPTLPLPSYVRVTNMENGISLVVRVNDRGPYHSNRLIDLSN 159 G I H + P Y R ++ GI V Y + + Sbjct: 96 GDLNIFMDHGQVVAPHYHRELDLSTGIVTVTYTIGGVQYTRELFVTYPD 144 >3iii_A COCE/NOND family hydrolase; structural genomics, center for structural genomics of infectious diseases, csgid; HET: MSE PLM; 1.95A {Staphylococcus aureus subsp} PDB: 3ib3_A* Length = 560 Score = 27.7 bits (60), Expect = 3.0 Identities = 18/85 (21%), Positives = 32/85 (37%), Gaps = 1/85 (1%) Query: 72 QIMGRWYVPRQYTAYAAVGMASWYGKAFHGRLTANGEVYGTEYITAAHPTLPLPSYVRVT 131 ++ + P + + V A YGK ++T G ++ T P S Sbjct: 53 KLYINIFRPNKDGKFPVVMSADTYGKDNKPKITNMGALWPTLGTIPTSSFTPEESPDPGF 112 Query: 132 NMENGISLVVRVNDRGPYHSNRLID 156 + N +VV+V RG S ++ Sbjct: 113 WVPNDY-VVVKVALRGSDKSKGVLS 136 >3hiq_A Vacuolar saporin; ribosome inactivating proteins, RIPS, hydrolase, plant defense, protein synthesis inhibitor, toxin; 2.19A {Saponaria officinalis} Length = 345 Score = 26.6 bits (58), Expect = 5.6 Identities = 8/46 (17%), Positives = 17/46 (36%), Gaps = 2/46 (4%) Query: 102 RLTANGEVYGTEYITAAHPTLPLPSYVRV--TNMENGISLVVRVND 145 + YG + + P ++RV +SL V+ ++ Sbjct: 112 DIKDPNLHYGGTNLPVIKRPVGPPKFLRVNLKASTGTVSLAVQRSN 157 >1m06_G G protein, GPG, major spike protein; bacteriophage, virion; HET: 3DR; 3.50A {Enterobacteria phage ALPHA3} SCOP: b.121.5.1 PDB: 1m0f_G 1rb8_G* Length = 187 Score = 26.8 bits (59), Expect = 6.1 Identities = 14/52 (26%), Positives = 21/52 (40%) Query: 104 TANGEVYGTEYITAAHPTLPLPSYVRVTNMENGISLVVRVNDRGPYHSNRLI 155 T N V ITA + L + + V+ +G +V D P N +I Sbjct: 30 TGNIPVINGGSITAERAVVNLYANMNVSTSSDGSFIVAMKVDTSPTDPNCVI 81 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.321 0.137 0.415 Gapped Lambda K H 0.267 0.0425 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,496,708 Number of extensions: 115626 Number of successful extensions: 263 Number of sequences better than 10.0: 1 Number of HSP's gapped: 261 Number of HSP's successfully gapped: 11 Length of query: 276 Length of database: 5,693,230 Length adjustment: 91 Effective length of query: 185 Effective length of database: 3,487,026 Effective search space: 645099810 Effective search space used: 645099810 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 56 (26.1 bits)